We consider the problem of learning a low dimensional representation for compositional data. Compositional data consists of a collection of nonnegative data that sum to a constant value. Since the parts of the collection are statistically dependent, many standard tools cannot be directly applied. Instead, compositional data must be first transformed before analysis. Focusing on principal component analysis (PCA), we propose an approach that allows low dimensional representation learning directly from the original data.

Instead,compositional datamust be first transformed before analysis.

Data augmentation plays a key role in modern machine learning pipelines. While numerous augmentation strategies have been studied in the context of computer vision and natural language processing, less is known for other data modalities. Our work extends the success of data augmentation to compositional data, i.e., simplex-valued data, which is of particular interest in microbiology, geochemistry, and other applications. Drawing on key principles from compositional data analysis, such as the \emph{Aitchison geometry of the simplex} and subcompositions, we define novel augmentation strategies for this data modality.

We consider the problem of learning a low dimensional representation for compositional data. Compositional data consists of a collection of nonnegative data that sum to a constant value. Since the parts of the collection are statistically dependent, many standard tools cannot be directly applied. Instead, compositional data must be first transformed before analysis. Focusing on principal component analysis (PCA), we propose an approach that allows low dimensional representation learning directly from the original data.

The analysis of spatial data from biological imaging technology, such as imaging mass spectrometry (IMS) or imaging mass cytometry (IMC), is challenging because of a competitive sampling process which convolves signals from molecules in a single pixel. To address this, we develop a scalable Bayesian framework that leverages natural sparsity in spatial signal patterns to recover relative rates for each molecule across the entire image. Our method relies on the use of a heavy-tailed variant of the graphical lasso prior and a novel hierarchical variational family, enabling efficient inference via automatic differentiation variational inference. Simulation results show that our approach outperforms state-of-the-practice point estimate methodologies in IMS, and has superior posterior coverage than mean-field variational inference techniques. Results on real IMS data demonstrate that our approach better recovers the true anatomical structure of known tissue, removes artifacts, and detects active regions missed by the standard analysis approach.

Gradient boosting has become a cornerstone of machine learning, enabling base learners such as decision trees to achieve exceptional predictive performance. While existing algorithms primarily handle scalar or Euclidean outputs, increasingly prevalent complex-structured data, such as distributions, networks, and manifold-valued outputs, present challenges for traditional methods. Such non-Euclidean data lack algebraic structures such as addition, subtraction, or scalar multiplication required by standard gradient boosting frameworks. To address these challenges, we introduce Fréchet geodesic boosting (FGBoost), a novel approach tailored for outputs residing in geodesic metric spaces. FGBoost leverages geodesics as proxies for residuals and constructs ensembles in a way that respects the intrinsic geometry of the output space. Through theoretical analysis, extensive simulations, and real-world applications, we demonstrate the strong performance and adaptability of FGBoost, showcasing its potential for modeling complex data.

High-dimensional compositional data, such as those from human microbiome studies, pose unique statistical challenges due to the simplex constraint and excess zeros. While dimension reduction is indispensable for analyzing such data, conventional approaches often rely on log-ratio transformations that compromise interpretability and distort the data through ad hoc zero replacements. We introduce a novel framework for interpretable dimension reduction of compositional data that avoids extra transformations and zero imputations. Our approach generalizes the concept of amalgamation by softening its operation, mapping high-dimensional compositions directly to a lower-dimensional simplex, which can be visualized in ternary plots. The framework further provides joint visualization of the reduction matrix, enabling intuitive, at-a-glance interpretation. To achieve optimal reduction within our framework, we incorporate sufficient dimension reduction, which defines a new identifiable objective: the central compositional subspace. For estimation, we propose a compositional kernel dimension reduction (CKDR) method. The estimator is provably consistent, exhibits sparsity that reveals underlying amalgamation structures, and comes with an intrinsic predictive model for downstream analyses. Applications to real microbiome datasets demonstrate that our approach provides a powerful graphical exploration tool for uncovering meaningful biological patterns, opening a new pathway for analyzing high-dimensional compositional data.

Data augmentation plays a key role in modern machine learning pipelines. While numerous augmentation strategies have been studied in the context of computer vision and natural language processing, less is known for other data modalities. Our work extends the success of data augmentation to compositional data, i.e., simplex-valued data, which is of particular interest in microbiology, geochemistry, and other applications. Drawing on key principles from compositional data analysis, such as the \emph{Aitchison geometry of the simplex} and subcompositions, we define novel augmentation strategies for this data modality. In particular, we set a new state-of-the-art for key disease prediction tasks including colorectal cancer, type 2 diabetes, and Crohn's disease.

High-dimensional compositional data are prevalent in many applications. The simplex constraint poses intrinsic challenges to inferring the conditional dependence relationships among the components forming a composition, as encoded by a large precision matrix. We introduce a precise specification of the compositional precision matrix and relate it to its basis counterpart, which is shown to be asymptotically identifiable under suitable sparsity assumptions. By exploiting this connection, we propose a composition adaptive regularized estimation (CARE) method for estimating the sparse basis precision matrix. We derive rates of convergence for the estimator and provide theoretical guarantees on support recovery and data-driven parameter tuning. Our theory reveals an intriguing trade-off between identification and estimation, thereby highlighting the blessing of dimensionality in compositional data analysis. In particular, in sufficiently high dimensions, the CARE estimator achieves minimax optimality and performs as well as if the basis were observed. We further discuss how our framework can be extended to handle data containing zeros, including sampling zeros and structural zeros. The advantages of CARE over existing methods are illustrated by simulation studies and an application to inferring microbial ecological networks in the human gut.

Data augmentation plays a key role in modern machine learning pipelines. While numerous augmentation strategies have been studied in the context of computer vision and natural language processing, less is known for other data modalities. Our work extends the success of data augmentation to compositional data, i.e., simplex-valued data, which is of particular interest in the context of the human microbiome. Drawing on key principles from compositional data analysis, such as the Aitchison geometry of the simplex and subcompositions, we define novel augmentation strategies for this data modality. Incorporating our data augmentations into standard supervised learning pipelines results in consistent performance gains across a wide range of standard benchmark datasets. In particular, we set a new state-of-the-art for key disease prediction tasks including colorectal cancer, type 2 diabetes, and Crohn's disease. In addition, our data augmentations enable us to define a novel contrastive learning model, which improves on previous representation learning approaches for microbiome compositional data. Our code is available at https://github.com/cunningham-lab/AugCoDa.